Comparative Genomics Analysis Reveals the Strain-specific Probiotic Potential and Putative Antimicrobial Peptides of...

Bifidobacterium breve is a dominant member of the infant gut microbiota and is widely recognized for its probiotic attributes, including carbohydrate metabolism, stress tolerance, and pathogen inhibition. In this study, we sequenced the whole genome of B. breve NCIM 5671 to assess its metabolic potential, adaptive traits, safety, and antimicrobial activity. We assembled the genome into 69 contigs totaling 2.41 Mb, with a GC content of 58.5%, and it encodes 2,189 genes. Functional annotation revealed a high abundance of genes involved in amino acid and carbohydrate metabolism. Pan-genome analysis of 50 B. breve genomes revealed an open pan-genome structure with 976 core genes and significant accessory and strain-specific gene diversity. Phylogenetic and ANI analyses placed NCIM 5671 within a clade of infant-derived strains. Notably, we identified multiple antimicrobial peptide biosynthetic gene clusters, including lanthipeptide and lasso peptide systems, some of which were previously reported in B. breve but remain functionally uncharacterized. In vitro analysis confirmed the production of a low-molecular-weight peptide with broad-spectrum antimicrobial activity, specifically inhibiting RNA biosynthesis, consistent with the known mechanism of lasso peptides. Safety assessment revealed no functional antibiotic resistance or virulence genes. Overall, this study establishes an integrated genomic and functional framework for elucidating strain-specific probiotic traits in NCIM 5671. Importantly, this is the first study to functionally explore a putative lasso peptide-associated antimicrobial system in B. breve.